Xiangshan Bay, the biggest marine aquaculture base in Zhejiang Province, is a semi- enclosed bay with slow water exchange rate. In the center of Xiangshan Bay lies Nansha Bay where a variety of mariculture models are applied. To better understand the structures and diversity of sediment microbial communities in different mariculture models, we constructed the 16S rDNA clone library for the analysis of samples from the shellfish culture, the seaweed culture and the fish cage culture. We obtained 136 OTUs from three sampling models that included 58 OTUs from the shellfish culture, 48 from the seaweed culture, and 57 from the fish cage culture. The distribution patterns of OTUs were highly different between the three sampling models which indicated the distinct microbial community structures. The calculation of species richness (Chao), evenness (ACE), and diversity (Shannon) were 245/739/3.8 (fish cage culture), 313/330/3.6 (shellfish culture) and 89/174/3.6 (seaweed culture) respectively. This suggested that the diversity of 16S rDNA gene clone libraries of seaweed culture model was the lowest among all three models. The results of the phylogenetic analysis showed that proteobacteria were the dominant microbes in all sampling models. The microbial community structure of the seaweed culture model differed obviously from those of the shellfish culture and the fish cage culture models. Rhizobium and some photosynthetic bacterial sequences were abundant in the seaweed culture clone library. Moreover, microbes closely related to sediment pollution were found in the fish cage culture model, such as Shigella, Escherichia, and ε-Proteobacteria. This implied that the fish cage culture could be the major source of pollution in the sediment of Nansha Bay.